Quantum dots (QDs) have been used extensively as fluorescent markers in several studies on living cells. Here, we report the synthesis of conjugates based on glutathione (GSH) and QDs (GSH-QDs) and we prove how these functionalized fluorescent probes can be used for staining a freshwater invertebrate called Hydra vulgaris. GSH is known to promote Hydra feeding response by inducing mouth opening. We demonstrate that GSH-QDs as well are able to elicit biological activity in such an animal, which results in the fluorescent staining of Hydra. GSH-QDs, once they reach the gastric region, are internalized by endodermal cells. The efficiency of GSH-QD internalization increases significantly when nanoparticles are coadministrated with free GSH. We also compared the behavior of bare QDs to that of GSH-QDs both in the presence and in the absence of free GSH. The conclusions from these series of experiments point to the presence of GSH binding proteins in the endodermal cell layer and uncover a novel role played by glutathione in this organism.